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I have a polygon grid (epsg:24381) from which I want to randomly select some polygons. Whenever I try to perform the sampling I'm getting the following error:

Error in h(simpleError(msg, call)): error in evaluating the argument 'obj' in selecting a method for function 'coordinates': cannot allocate vector of size 5 Kb Error during wrapup: cannot allocate vector of size 1.7 Mb Error: no more error handlers available (recursive errors?); invoking 'abort' restart.

Here is the code and the package I'm utilizing is spatialEco, R v4.4.1, RStudio v1.4.1717, Windows 10.

shp <- ("xxx/grid.shp") %>%
  st_read()

#convert shp to spatialpolygondataframe
spdf <- as_Spatial(shp)

#random polygon selection from a grid polygon
random_poly = sample.poly(spdf, n = 300, type = "random")

What might cause the problem?

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  • That's a weird one, can you post your data up somewhere so I can figure out what may be going on? Aug 11, 2021 at 19:59
  • easyupload.io/xfv7d7 password: covid21
    – Nikos
    Aug 11, 2021 at 21:01

2 Answers 2

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I cannot replicate this error so, I imagine, as the error indicates, you are actually running out of memory. Besides reading in the grid, with 229,374 polygons you are trying to create 68,812,200 sample points. A few things to check are how much RAM you have and if you are running the 64-bit version of R (within RStudio). I would note that a computer with even a relatively small amount of RAM (4GB) should be able to hand this problem leading me to think that you are running 32-bit R or having RAM allocated elsewhere (another process).

Here is the code that I used and it is running fine with R 4.1.0 x86_64-w64-mingw32/x64, sf_1.0-2, sp_1.4-5 and spatialEco_1.3-7.

library(spatialEco)
library(sp)
library(sf)

shp <- as(sf::st_read("C:/test/grid.shp"), "Spatial")
random_poly = sample.poly(shp, n = 300, type = "random")

You can proof the code by reducing the size of your problem.

( random_poly = sample.poly(shp[sample(1:nrow(shp), 10),], 
                            n = 10, type = "random") ) 

This opens the door to subsampling your problem down. In a loop, you can grab a few thousand polygons at a time, create a sample and write them out. The sf::st_write function has an append argument that will allow you to add to iteratively append a shapefile on disk. Something along these lines should work, will take awhile but control memory usage.

( n=round(nrow(shp) /20, 0) )
g <- split(1:nrow(shp), ceiling(seq_along(1:nrow(shp)) / n))

st_write(as(sample.poly(shp[g[[1]],], n = 300, type = "random"),
         "sf"), "sample_pts.shp")  

lapply(g[-1], function(x) {  
  st_write(as(sample.poly(shp[x,], n = 300, 
           type = "random"), "sf"),
           "sample_pts.shp",
           append=TRUE) })
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  • Dear Jeffrey, first of all you were right about the R version on my laptop. I had the 32bit installed. So I re-installed it and I dl the R 4.1.1 x86_64-w64-mingw32/x64. Unfortunately the same error persists despite the control memory usage you told me to try. I will try and tune the parameters and I'll come back again with an answer.
    – Nikos
    Aug 12, 2021 at 9:25
  • 1
    @niktziok by default both versions are installed. If you are using RStudio, you have to configure the software to aim at the correct version. I would highly recommend trying to run this problem in R. I have had numerous experiences with RStudio not playing well with sp class objects, with very strange behavior. It seems to be better with more recent versions but, I still expect occasional issues to arise. When running into issues, always revert to R to test solutions thus, taking an additional software out of the equation. Make sure that you are launching R x64. Aug 12, 2021 at 14:23
0

I can not access the file you made available (network issues). But maybe the following helps - selecting the polygons in sf before converting to SPDF

library (sf)
library (sp)
library (dplyr)

sourceFile <- 'grid.shp'
sampleSize <- 300

#read in the source file
dt <- st_read (sourceFile)

# generate a sample of size 'sampleSize' from the row numbers of the polygons in the grid
s <- sample(c(1:nrow (dt)), sampleSize)

# copy over the polygons into your sample and convert to SPDF
random_poly <- dt[s,] %>% as_Spatial()

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